In my opinion, 3 things in particular that were wrong with 2nd season :
The opening (...?)
Chiaki's haircolour (carried over to the 3rd season) (...?)
It just wasn't that funny (....?)
Good to see you're backing your opinions up.
I win by default.
Allow me to elaborate
The opening- Ok wtf? That doesn't fit the show at all, it feels like a really bad parody of something else.
(got a little mixed up)- In the manga she was blonde as well is in the 2nd season but not the 1st season. Though she was still better with brown hair. The problem was the hairstyle, you know how it the 1st season the little bit on the top of her head had a mind of it's own? None of that in the other 2 seasons.
It just wasn't the funny- This is opinion based but I'm sure most would agree that the 2nd season just wasn't that funny.
Though the main annoyance is that the company that made the 2nd season changed way to much from the 1st season
A couple of examples:
Kana somehow got way bigger breasts
Chiaki's hair no longer had a mind of it's own and the colour was changed
There are a bunch of other little things but it's been so long since I watched the 2nd season that I can't remember them all.